Artemis

Homepage:http://www.sanger.ac.uk/Software/Artemis/Version: Release 6 License:GPLDescription:Description:
Artemis is a free genome viewer and annotation tool that allows visualization of sequence
features and the results of analyses within the context of the sequence, and its six-frame
translation. It can read complete EMBL and GENBANK database entries
or sequence in FASTA or raw format. Extra sequence features can be in EMBL, GENBANK or GFF
format.
Online ManualFAQsExamples

Bioperl

Homepage:http://www.bioperl.org/Version: 1.4 License:ArtisitcDescription:
The Bioperl project is a coordinated effort to collect computational methods routinely
used in bioinformatics into a set of standard CPAN-style, well-documented, and freely
available Perl modules. TutorialFAQs

ClustalX

Homepage:http://www-igbmc.u-strasbg.fr/BioInfo/ClustalX/Top.htmlVersion: 1.83 License:click
hereDescription:
Clustal X is a graphical interface for the ClustalW multiple sequence alignment program.
It provides an integrated environment for performing multiple sequence and profile
alignments and analyzing the results. The sequence alignment is displayed in a window on
the screen. A versatile coloring scheme has been incorporated allowing you to highlight
conserved features in the alignment. The pull-down menus at the top of the window allow
you to select all the options required for traditional multiple sequence and profile
alignment.

User can cut-and-paste sequences to change the order of the alignment; you can select a
subset of sequences to be aligned; you can select a sub-range of the alignment to be
realigned and inserted back into the original alignment.

Alignment quality analysis can be performed and low-scoring segments or exceptional
residues can be highlighted.

Garlic

Homepage:http://garlic.mefos.hr/garlic/Version: 1.4 License:GPLDescription:
Garlic is a molecular visualization program. It's written for the investigation of membrane proteins. It may be used to visualize other proteins, as well as some geometric objects. The included version of garlic recognizes PDB format version 2.1. Garlic may also be used to analyze protein sequences.Documentation

Ghemical

Homepage:http://www.uku.fi/~thassine/ghemical/Version: 1.01License:GPLDescription:
Ghemical a very versatile simulation engine for molecular modeling and quantum-mechanical calculations. Its friendly GUI is suitable for beginners.

Glimmer

Homepage:http://www.tigr.org/software/glimmer/Version: 2.13 License:ArtisticDescription:
Glimmer is a system for finding genes in microbial DNA, especially the genomes of
bacteria, archaea, and viruses. Glimmer (Gene Locator and Interpolated Markov Modeler)
uses interpolated Markov models (IMMs) to identify the coding regions and distinguish them
from noncoding DNA. The IMM approach uses a combination of Markov
models from 1st through 8th-order, weighting each model according to its predictive power.
Glimmer use 3-periodic nonhomogenous Markov models in their IMMs.

GROMACS

Homepage:http://www.gromacs.org/Version: 3.2.1 License:GPLDescription:
GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.

It is primarily designed for biochemical molecules like proteins and lipids that have a lot of complicated bonded interactions, but since GROMACS is extremely fast at calculating the nonbonded interactions (that usually dominate simulations) many groups are also using it for research on non-biological systems, e.g. polymers.
Online ManualTutorialsFAQs

GP/Arka

Homepage:http://bioinformatics.org/genpak/index.htmlVersion: GP 0.26, Arka 0.11 License:GPLDescription:
GP and Arka are very leightweighed programs for manipulation of DNA/RNA/protein
sequences. They are designed on one hand to run smoothly on older machines, and on the
other -- to faciliate processing of large numbers of sequence/data files. GP includes
utilities to convert DNA/RNA to protein, determine codon usage/GC contents, promotor
searches, Tm, searching for restriction sites, converting sequences into numerical
representations and much more.

GP is a set of small utilities written in ANSI C to manipulate DNA sequences in a Unix
fashion, fit for combining within shell and cgi scripts.

Arka is a program that serves as a graphical interface for the programs from the GP
package.

MUMmer

Homepage:http://www.tigr.org/software/mummer/Version: 3.15 License:ArtisticDescription:
MUMmer is a system for rapidly aligning entire genomes, whether in complete or draft form.
For example, MUMmer 3.0 can find all 20-basepair or longer exact matches between a pair of
5-megabase genomes in 13.7 seconds, using 78 MB of memory, on a 2.4 GHz Linux desktop
computer. MUMmer can also align incomplete genomes; it handles the 100s or 1000s of
contigs from a shotgun sequencing project with ease, and will align them to another set of
contigs or a genome using the NUCmer program included with the system. If the species are
too divergent for DNA sequence alignment to detect similarity, then the PROmer program can
generate alignments based upon the six-frame translations of both input sequences.
Manual

NCBI
Toolkit

Reference Web-site:
http://www.ncbi.nlm.nih.gov/BLAST/Version: 6.1.20041020-2 License:Click hereDescription:
The NCBI (National Center for Biotechnology Information) Software Development Toolkit was developed for the production and
distribution of GenBank, Entrez, BLAST, and related services by NCBI.

PyMOL

Homepage:http://pymol.sourceforge.net/Version: 0.97 License:click hereDescription:
PyMOL is a molecular graphics system with an embedded Python interpreter designed for real-time visualization and rapid generation of high-quality molecular graphics images and animations. It can also perform many other valuable tasks (such as editing PDB files) to assist you in your research.ManualsFAQsUseful scripts

The Ramachandran Plot Explorer

Homepage:
http://www.dillgroup.ucsf.edu/~bosco/rama.htmlVersion: 0.9 License:GPLDescription:
The Ramachandran Plot Explorer really does offer something new. It has been specially
designed to focus solely on the phi, psi and chi angles. It can also easily:
explore conformation changes
explore secondary structure and common loop structures
construct and edit protein sequences interactively

Rasmol

Homepage:http://www.umass.edu/microbio/rasmol/index2.htmVersion: 2.7.2.1.1 License:click
hereDescription: RasMol is a molecular graphics program intended for the visualisation
of proteins, nucleic acids and small molecules. The program is aimed at display,
teaching and generation of publication quality images. The program has been
developed at the University of Edinburgh's Biocomputing Research Unit and the
Biomolecular Structure Department at Glaxo Research and Development, Greenford, UK.

RasMol reads in molecular co-ordinate files in a number of formats and interactively
displays the molecule on the screen in a variety of colour schemes and
representations.

Raster3D

Homepage:
http://www.bmsc.washington.edu/raster3d/raster3d.htmlVersion: 2.7c License: Binaries only for VigyaanCDDescription:
Raster3D is a set of tools for generating high quality raster images of proteins or other
molecules. The core program renders spheres, triangles, cylinders, and quadric surfaces
with specular highlighting, Phong shading, and shadowing. It uses an efficient software
Z-buffer algorithm which is independent of any graphics hardware. Ancillary programs
process atomic coordinates from PDB files into rendering descriptions for pictures
composed of ribbons, space-filling atoms, bonds, ball+stick, etc. Raster3D can also be
used to render pictures composed in other programs such as Molscript in glorious 3D with
highlights, shadowing, etc. Output is to pixel image files with 24 bits of color
information per pixel.FAQsOnline
documentationSample
figures

TINKER

Homepage:
http://dasher.wustl.edu/tinker/Version: 4.2 License:Binaries only for VigyaanCDImportant Note: TINKER version included on VigyaanCD should be considered as a trial version. Users
planning to use TINKER on a regular basis, should obtain a copy from the TINKER homepage and are also requested to register their copy.Description:
The TINKER molecular modeling software is a complete and general package for
molecular mechanics and dynamics, with some special features for biopolymers. TINKER has
the ability to use any of several common parameter sets, such as Amber (ff94, ff96, ff98
and ff99), CHARMM (19 and 27), Allinger MM (MM2-1991 and MM3-2000), OPLS (OPLS-UA, OPLS-AA
and OPLS-AA/L). Parameter sets for other standard force fields such as UFF, ENCAD and MM4
are under consideration. In addition, we are actively developing our own AMOEBA force
field based upon polarizable atomic multipole electrostatics.
The TINKER package
includes a variety of novel algorithms such as a new distance
geometry metrization method that has greater speed and better sampling than standard
methods, Elber's reaction path methods, several of our Potential Smoothing and Search
(PSS) methods for global optimization, an efficient potential surface scanning procedure,
a flexible implementation of atomic multipole-based electrostatics with explicit dipole
polarizability, a selection of continuum solvation treatments including several variants
of the generalized Born (GB/SA) model, an efficient truncated Newton (TNCG) local
optimizer, surface areas and volumes with derivatives, a simple free energy perturbation
facility, normal mode analysis, minimization in Cartesian, torsional or rigid body space,
velocity Verlet stochastic dynamics, an improved spherical energy cutoff method, Particle
Mesh Ewald summation for partial charges and regular Ewald for polarizable multipoles, a
novel reaction field treatment of long range electrostatics, and more....Note: The doc, examples and params directories of TINKER are available on VigyaanCD
in the directory:
/usr/local/share/tinker